Contacts of the strand formed by residues 106 - 111 (chain P) in PDB entry 1KYO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 106 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105P LYS* 1.3 82.9 - - - +
107P VAL* 1.3 63.9 + - - +
108P VAL* 5.3 4.9 - - + +
117P PHE* 6.4 2.0 - - + -
118P ILE 3.6 3.9 + - - +
119P ARG* 2.8 58.6 + - - +
168P GLY* 4.0 3.7 - - - -
169P GLU* 4.0 20.5 + - - +
176P TRP* 3.4 30.3 + - + +
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Residues in contact with VAL 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96P VAL* 5.1 1.1 - - + -
101P ILE* 3.6 38.1 - - + -
106P ASN* 1.3 75.1 - - - +
108P VAL* 1.3 74.3 + - - +
109P VAL* 4.5 16.2 - - + -
116P VAL 3.6 1.4 - - - +
117P PHE* 3.7 1.7 - - - -
118P ILE* 2.9 46.9 + - + +
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Residues in contact with VAL 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LEU* 4.6 23.4 - - + +
106P ASN* 5.3 4.5 - - + +
107P VAL* 1.3 85.7 - - - +
109P VAL* 1.3 66.7 + - - +
115P PRO* 4.0 20.4 - - + -
116P VAL 3.5 4.5 - - - +
117P PHE* 3.9 34.3 - - + -
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Residues in contact with VAL 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C LEU* 5.0 2.7 - - - -
94P VAL* 5.2 8.7 - - + -
96P VAL* 4.1 41.3 - - + -
107P VAL* 4.5 13.7 - - + -
108P VAL* 1.3 79.4 - - - +
110P LYS* 1.3 64.1 + - - +
115P PRO* 3.7 2.9 - - - +
116P VAL* 2.7 55.6 + - + +
118P ILE* 4.5 3.8 - - + -
214P VAL* 5.6 0.2 - - + -
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Residues in contact with LYS 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C PRO* 6.2 4.3 - - + -
263C LEU* 4.2 30.1 - - + +
94P VAL* 4.4 17.0 - - - +
109P VAL* 1.3 74.5 - - - +
111P TRP* 1.3 64.6 + - - +
112P GLN 4.2 1.1 - - - +
113P GLY* 3.9 31.9 - - - +
114P LYS 3.9 2.7 - - - -
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Residues in contact with TRP 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P MET* 5.3 0.9 - - + -
92P ALA* 3.0 36.4 + - + -
93P LYS 4.5 0.2 - - - -
94P VAL* 4.0 24.2 - - + -
109P VAL 4.0 0.2 + - - -
110P LYS* 1.3 75.8 - - - +
112P GLN* 1.3 100.1 + - - +
113P GLY 3.4 0.2 - - - -
114P LYS* 3.0 31.3 + - - +
116P VAL* 3.7 18.2 - - + -
156P LEU* 4.1 32.3 - - + -
203P PRO* 4.4 13.0 - - + -
204P ALA 5.8 1.6 - - - -
214P VAL* 4.2 11.4 - - + -
215P GLY* 3.7 28.0 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il